Added license notice headers

src/arg_parser.h

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #pragma once
 #include <iostream>
 #include <stdio.h>

src/depth.cpp

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #include "depth.h"
 #include <iostream>
 

src/depth.h

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #pragma once
 #include <algorithm>
 #include <fstream>
@@ -5,7 +23,7 @@
 #include <string>
 #include <unordered_map>
 #include <vector>
-#include "depth_table.h"
+#include "table_parser.h"
 #include "parameters.h"
 #include "popmap.h"
 #include "utils.h"

src/distrib.cpp

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #include "distrib.h"
 
 void distrib(Parameters& parameters) {

src/distrib.h

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #pragma once
 #include <fstream>
 #include <string>
 #include <unordered_map>
 #include <vector>
-#include "depth_table.h"
+#include "table_parser.h"
 #include "stats.h"
 #include "parameters.h"
 #include "popmap.h"

src/freq.cpp

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #include "freq.h"
 
 

src/freq.h

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #pragma once
 #include <fstream>
 #include <string>
 #include <unordered_map>
 #include <vector>
-#include "depth_table.h"
+#include "table_parser.h"
 #include "parameters.h"
 #include "popmap.h"
 #include "utils.h"

src/main.cpp

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #include "arg_parser.h"
 #include "depth.h"
 #include "distrib.h"

src/map.cpp

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #include "map.h"
 
 

src/map.h

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #pragma once
 #include <fstream>
 #include <string>
@@ -5,7 +23,7 @@
 #include <vector>
 #include "bwa/bwamem.h"
 #include "bwa/kseq.h"
-#include "depth_table.h"
+#include "table_parser.h"
 #include "parameters.h"
 #include "popmap.h"
 #include "stats.h"

src/parameters.h

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #pragma once
 #include <string>
 

src/popmap.cpp

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #include "popmap.h"
 
 Popmap load_popmap(Parameters& parameters, bool compare) {

src/popmap.h

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #pragma once
 #include <unordered_map>
 #include "parameters.h"

src/process.cpp

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #include "process.h"
 
 KSEQ_INIT(gzFile, gzread) // Kseq init macro

src/process.h

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #pragma once
 #include <dirent.h>
 #include <iostream>

src/signif.cpp

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #include "signif.h"
 
 void signif(Parameters& parameters) {

src/signif.h

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #pragma once
 #include <fstream>
 #include <string>
 #include <unordered_map>
 #include <vector>
-#include "depth_table.h"
+#include "table_parser.h"
 #include "parameters.h"
 #include "popmap.h"
 #include "stats.h"

src/stats.cpp

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #include "stats.h"
 
 double get_chi_squared_p(double chi_squared) {

src/stats.h

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #pragma once
 #include "kfun/kfun.h"
 #include "utils.h"

src/subset.cpp

+/*
+* Copyright (C) 2020 Romain Feron
+* This file is part of RADSex.
+
+* RADSex is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+
+* RADSex is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+
+* You should have received a copy of the GNU General Public License
+* along with RADSex.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
 #include "subset.h"
 
 void subset(Parameters& parameters) {